Vitamin D response element gene transcriptions: Difference between revisions

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Positive strand, positive direction: TGAACT at 4016, GGGTCA at 3379, GGGTCA at 3082, AGTTCA at 2616, GGTTCA at 2594, AGTTCA at 2509, GGGTCA at 2024, TGACCC at 1954, GGGTCA at 1250, TGACCC at 348.
Positive strand, positive direction: TGAACT at 4016, GGGTCA at 3379, GGGTCA at 3082, AGTTCA at 2616, GGTTCA at 2594, AGTTCA at 2509, GGGTCA at 2024, TGACCC at 1954, GGGTCA at 1250, TGACCC at 348.
==Acknowledgements==
The content on this page was first contributed by: Henry A. Hoff.


==See also==
==See also==
{{div col|colwidth=20em}}
{{div col|colwidth=20em}}
* [[A1BG gene transcription core promoters]]
* [[A1BG gene transcriptions]]
* [[A1BG regulatory elements and regions]]
* [[A1BG response element gene transcriptions]]
* [[A1BG response element negative results]]
* [[A1BG response element positive results]]
* [[Complex locus A1BG and ZNF497]]
* [[Complex locus A1BG and ZNF497]]
* [[Transcription factor]]
{{Div col end}}
{{Div col end}}


Revision as of 22:43, 9 March 2021

Associate Editor(s)-in-Chief: Henry A. Hoff

Vitamin D response elements (VDRE) typically consist of two conserved hexameric half-sites separated by a three nucleotide spacer, referred to as a DR3 type element.[1] Although it is known that the sequence of a VDRE can have a strong influence on the degree of protein binding, particularly at the fifth position in the half-site,[2] previous studies have focused on synthetic variations of response elements and not naturally occurring sequences.[3]

The VDR is widely distributed in tissues, and is not restricted to those tissues considered the classic targets of vitamin D. The VDR upon binding to 1,25(OH)2D heterodimerizes with other nuclear hormone receptors, in particular the family of retinoid X receptors. This complex then binds to special DNA sequences called vitamin D response elements (VDRE) in the promoters of genes which it regulates. A variety of additional proteins called coactivators complex with the activated VDR/RXR heterodimers either to form a bridge from the VDR/RXR complex binding to the VDRE to the proteins responsible for transcription such as RNA polymerase II binding to the transcription start site or to help unravel the chromatin at the site of the gene via recruitment of histone acetyl transferases (HAT), allowing transcription to proceed.[4]

Human genes

Consensus sequences

"The following VDRE oligonucleotides were used: mouse osteopontin, 5′-GCTCGGGTAGGGTTCACGAGGTTCACTCGACTCG-3′; DR3, 5′-GCTCGGGTAGAGGTCAAGGAGGTCACTCGACTCG-3′; DR3′, 5′-GCTCGGGTAGAGTTCAAGGAGTTCACTCGACTCG-3′; human osteocalcin, 5′-GCTCGGGTAGGGGTGACTCACCGGGTGAACGGGGGCATCTCGACTCG-3′; and Random, 5′-GCTCGGGTAGCTAATCCGTTTCGAGCTCGACTCG-3′."[5]

"Using the Jasper and Consite algorithms, the A/GGG/TTCAnnnA/GGG/TTCA and GA/GGTTCATnnnGTTCA sequences were considered as human and mouse VDRE consensus sequences, respectively, as previously shown.17, 18 Previous studies have suggested that regulatory VDREs could locate distally, i.e. > 1 Mb, to the transcription starting site.19 We analysed the entire genomic sequence of the human and murine HOTAIR and ANRIL genes as well as 5 kb upstream the transcription starting sites to include proximal promoter regions. Our analysis revealed two and three potential VDREs in the human HOTAIR and ANRIL genes, respectively, all of them were located within the intron 1 [...]."[6]

Consensus sequences: (A/G)G(G/T)TCA (human) and G(A/G)GTTCAT (mouse) in (A/G)G(G/T)TCANNN(A/G)G(G/T)TCA and G(A/G)GTTCATNNNGTTCA.

VDRE samplings

Copying the consensus of the VDRE: (A/G)G(G/T)TCA and putting the sequence in "⌘F" finds no locations for this sequence between ZSCAN22 and A1BG but there three between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/G)G(G/T)TCA (starting with SuccessablesVDRE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for (A/G)G(G/T)TCA, 2, AGGTCA at 1532, AGGTCA at 1352.
  2. positive strand, negative direction, looking for (A/G)G(G/T)TCA, 12, AGGTCA at 4307, AGTTCA at 4176, AGTTCA at 4025, AGGTCA at 2585, AGGTCA at 2248, AGTTCA at 1178, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439, AGTTCA at 254, GGGTCA at 206.
  3. positive strand, positive direction, looking for (A/G)G(G/T)TCA, 7, GGGTCA at 3379, GGGTCA at 3082, AGTTCA at 2616, GGTTCA at 2594, AGTTCA at 2509, GGGTCA at 2024, GGGTCA at 1250.
  4. negative strand, positive direction, looking for (A/G)G(G/T)TCA, 5, AGGTCA at 4269, AGTTCA at 4201, GGGTCA at 3820, AGGTCA at 2220, AGGTCA at 153.
  5. complement, negative strand, negative direction, looking for (C/T)C(A/C)AGT, 12, TCCAGT at 4307, TCAAGT at 4176, TCAAGT at 4025, TCCAGT at 2585, TCCAGT at 2248, TCAAGT at 1178, TCCAGT at 712, TCCAGT at 576, TCCAGT at 568, TCCAGT at 439, TCAAGT at 254, CCCAGT at 206.
  6. complement, positive strand, negative direction, looking for (C/T)C(A/C)AGT, 2, TCCAGT at 1532, TCCAGT at 1352.
  7. complement, positive strand, positive direction, looking for (C/T)C(A/C)AGT, 5, TCCAGT at 4269, TGAAGT at 4201, CCCAGT at 3820, TCCAGT at 2220, TCCAGT at 153.
  8. complement, negative strand, positive direction, looking for (C/T)C(A/C)AGT, 7, CCCAGT at 3379, CCCAGT at 3082, TCAAGT at 2616, CCAAGT at 2594, ACTAGT at 2509, CCCAGT at 2024, CCCAGT at 1250.
  9. inverse complement, negative strand, negative direction, looking for TGA(A/C)C(C/T), 11, TGAACC at 4268, TGAACT at 4012, TGACCC at 3750, TGAACT at 3242, TGAACT at 3103, TGAACC at 2921, TGAACT at 2580, TGAACT at 2127, TGAACC at 1927, TGAACT at 1300, TGAACC at 328.
  10. inverse complement, positive strand, negative direction, looking for TGA(A/C)C(C/T), 8, TGAACC at 3784, TGAACC at 3245, TGAACC at 2717, TGAACC at 2382, TGAACC at 1956, TGAACC at 1303, TGAACC at 1012, TGAACC at 846.
  11. inverse complement, positive strand, positive direction, looking for TGA(A/C)C(C/T), 3, TGAACT at 4016, TGACCC at 1954, TGACCC at 348.
  12. inverse complement, negative strand, positive direction, looking for TGA(A/C)C(C/T), 6, TGACCC at 4217, TGACCT at 4019, TGAACC at 3937, TGAACC at 3838, TGACCA at 3785, TGACCC at 1663.
  13. inverse negative strand, negative direction, looking for ACT(G/T)G(A/G), 8, ACTTGG at 3784, ACTTGG at 3245, ACTTGG at 2717, ACTTGG at 2382, ACTTGG at 1956, ACTTGG at 1303, ACTTGG at 1012, ACTTGG at 846.
  14. inverse positive strand, negative direction, looking for ACT(G/T)G(A/G), 11, ACTTGG at 4268, ACTTGA at 4012, ACTGGG at 3750, ACTTGA at 3242, ACTTGA at 3103, ACTTGG at 2921, ACTTGA at 2580, ACTTGA at 2127, ACTTGG at 1927, ACTTGA at 1300, ACTTGG at 328.
  15. inverse positive strand, positive direction, looking for ACT(G/T)G(A/G), 6, ACTGGG at 4217, ACTGGA at 4019, ACTTGG at 3937, ACTTGG at 3838, ACTGGA at 3785, ACTGGG at 1663.
  16. inverse negative strand, positive direction, looking for ACT(G/T)G(A/G), 3, ACTTGA at 4016, ACTGGG at 1954, ACTGGG at 348.

VDRE UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: TGAACC at 4268, TGAACT at 4012, TGACCC at 3750, TGAACT at 3242, TGAACT at 3103, TGAACC at 2921.

Positive strand, negative direction: AGGTCA at 4307, AGTTCA at 4176, AGTTCA at 4025, TGAACC at 3784, TGAACC at 3245.

VDRE core promoters

Main article: Core promoter gene transcriptions

Negative strand, positive direction: AGGTCA at 4269.

VDRE proximal promoters

Main article: Proximal promoter gene transcriptions

Positive strand, negative direction: TGAACC at 2717.

Negative strand, positive direction: TGACCC at 4217, AGTTCA at 4201.

VDRE distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TGAACT at 2580, TGAACT at 2127, TGAACC at 1927, AGGTCA at 1532, AGGTCA at 1352, TGAACT at 1300, TGAACC at 328.

Positive strand, negative direction: AGGTCA at 2585, TGAACC at 2382, AGGTCA at 2248, TGAACC at 1956, TGAACC at 1303, AGTTCA at 1178, TGAACC at 1012, TGAACC at 846, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439, AGTTCA at 254, GGGTCA at 206.

Negative strand, positive direction: TGACCT at 4019, TGAACC at 3937, TGAACC at 3838, GGGTCA at 3820, TGACCA at 3785, AGGTCA at 2220, TGACCC at 1663, AGGTCA at 153.

Positive strand, positive direction: TGAACT at 4016, GGGTCA at 3379, GGGTCA at 3082, AGTTCA at 2616, GGTTCA at 2594, AGTTCA at 2509, GGGTCA at 2024, TGACCC at 1954, GGGTCA at 1250, TGACCC at 348.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

References

  1. ↑ Roff A, Wilson RT (March 2009). "A Novel SNP in a Vitamin D Response Element of the CYP24A1 Promoter Reduces Protein Binding, Transactivation, and Gene Expression". Journal of Steroid Biochem Mol Biol. 112 (1–3): 47–54. doi:10.1016/j.jsbmb.2008.08.009. PMC 2749287. PMID 18824104.
  2. ↑ Jin CH, Pike JW (1996). "Human vitamin D receptor-dependent transactivation in Saccharomyces cerevisiae requires retinoid X receptor". Mol. Endocrinol. 10 (2): 196–205. doi:10.1210/mend.10.2.8825559. PMID 8825559.
  3. ↑ Umesono K, Murakami KK, Thompson CC, Evans RM (28 June 1991). "HDirect repeats as selective response elements for the thyroid hormone, retinoic acid, and vitamin D3 receptors". Cell. 65 (7): 1255–66. doi:10.1016/0092-8674(91)90020-Y. PMC 6159884. PMID 1648450.
  4. ↑ Daniel Bikle (2014). Kenneth R Feingold, Bradley Anawalt, Alison Boyce, George Chrousos, Wouter W de Herder, Kathleen Dungan, Ashley Grossman, Jerome M Hershman, Hans J Hofland, Gregory Kaltsas, Christian Koch, Peter Kopp, Márta Korbonits, Robert McLachlan, John E Morley, Maria New, Jonathan Purnell, Frederick Singer, Constantine A Stratakis, Dace L Trence, Don P Wilson, ed. Vitamin D: Production, Metabolism, and Mechanisms of Action, In: Endotext. South Dartmouth (MA): MDText.com, Inc. PMID 25905172.
  5. ↑ Theodore A. Craig, Timothy D. Veenstra, Stephen Naylor, Andy J. Tomlinson, Kenneth L. Johnson, Slobodan Macura, Nenad Juranić, and Rajiv Kumar (26 August 1997). "Zinc Binding Properties of the DNA Binding Domain of the 1,25-Dihydroxyvitamin D3 Receptor". Biochemistry. 36 (34): 10482–10491. doi:10.1021/bi970561b. PMID 9265628. Retrieved 4 September 2020.
  6. ↑ Majid Pahlevan Kakhki, Abbas Nikravesh, Zeinab Shirvani Farsani, Mohammad Ali Sahraian, Mehrdad Behmanesh (April 2018). "HOTAIR but not ANRIL long non‐coding RNA contributes to the pathogenesis of multiple sclerosis". Immunology. 153 (4): 479–487. doi:10.1111/imm.12850. Retrieved 8 March 2021.

External links

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